Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions
Institution: Institut Pasteur
This plugin contains 4 functional and independent blocks that performs SODA analysis in standard (widefield, confocal, structured-illumination…) and localization-based (STORM, PALM, DNA-PAINT…) microscopy.
Webinars about SODA
Advanced SMLM colocalization webinar from the NEUBIAS Academy (English). Part 2 by Thibault Lagache (at 00:47:39) is on Statistical tools for analyzing the spatial distribution of objects with a demo on the SODA plugin.
Colocalisation analysis with the Icy plugin SODA, webinar from the RT MFM network (French), with explanations on the SODA plugin
Details of the method and algorithm are given in
– Block SODA
List of detections 1 & 2: spots (ROIs) corresponding to detections from channel or sequence 1 & 2
Input sequences: respective sequences of detections 1 & 2. Input sequences are used to compute the intensity centers (i.e. positions) of detections 1 & 2
ROI of analysis (cell’s shape) This key parameter corresponds to the ROI where SODA analysis is performed. If this ROI is too large, detections might appear as coupled (colocalized) while they are not..
Max. Radius and Step Max distance and step for computing the Ripley’s K function (see original article for details)
Fixed search distance: If selected, the plugin will simply count the number of detections 2 at distances 0, step,..,i*step,..Max. radius from detections 1
Example of protocol:
Simple protocol analyzing the coupling between 2 populations of spots (a third channel is used to automatically determine the cell’s ROI)
Demo video Simple protocol
-Blocks SODA STORM 2D&3D
-Block SODA suite